User: chriad

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chriad10
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8 months, 2 weeks ago
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2 years, 1 month ago
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c***********************@fmi.ch

Posts by chriad

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problems when working with SingleCellExperiment object in scater
... Hi, I have a SingleCellExperiment object: class: SingleCellExperiment dim: 27998 3265 metadata(0): assays(1): counts rownames(27998): ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000096730 ENSMUSG00000095742 rowData names(2): id symbol colnames: NULL colData names(2): dataset barcode reduce ...
scater singlecellexperiment written 8 months ago by chriad10 • updated 8 months ago by davis90
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Plotting several heatmaps onto the same grid with the ComplexHeatmap package in R
... My question is related to this one: http://stackoverflow.com/questions/13081310/combining-multiple-complex-plots-as-panels-in-a-single-figure I also have a unsatisfactory solution based on the answer to the above questions. I'd like a plot like this: I use the following code for this figure: ...
complexheatmap written 21 months ago by chriad10 • updated 21 months ago by jokergoo110
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Error in summarizeOverlaps: Error in names(res) <- nms; 'names' attribute [15] must be the same length as the vector [2]
... Edit: One of my bam files has size 0 on disk! I get the following error when I call summarizeOverlpas:   Error in names(res) <- nms :   'names' attribute [15] must be the same length as the vector [2] Calls: summarizeOverlaps ... .dispatchBamFiles -> bplapply -> bplapply -> bplapply - ...
biocparallel software error summarizeoverlaps written 21 months ago by chriad10
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csaw with negative controls
... Say I'd like to assess 'differential binding' of a histon mark (K9me2) in two conditions (mutant vs wildtype), So I try to answer the question how much binding of the histon mark changes when changing from wlidtype to mutant. I have 2 replicates for each condition, each with a matching input (8 lib ...
csaw written 23 months ago by chriad10
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Comment: C: csaw filterWindows function results in a warning: ("Zero library size detected."
... I use filter=0 in windowCounts, because I had to parallelize and filter!=0 would result in SummarizedExperiment instances with different row counts that couldn't be joined afterwards: WIDTH=10000 se <- mclapply(X=Rsamtools::path(bfl), FUN=windowCounts, param=param.csaw, bin=T, width=WIDTH, filt ...
written 2.1 years ago by chriad10
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csaw filterWindows function results in a warning: ("Zero library size detected.")
... I have a summarizedExperiment with ChIP and input counts and I'd like to use the filterWindows function.   > s641 class: RangedSummarizedExperiment dim: 10030 2 metadata(48): spacing width ... shift final.ext assays(1): counts rownames: NULL rowData names(1): mappableFractionPerRange colname ...
csaw written 2.1 years ago by chriad10 • updated 2.1 years ago by Aaron Lun19k

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Popular Question 18 months ago, created a question with more than 1,000 views. For Plotting several heatmaps onto the same grid with the ComplexHeatmap package in R

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